Primary Consideration

Due to the controversial nature that this specific problem represents, it takes a mature player and a mature DM to handle this specific scenario well. Ensure that the player and DM have a conversation about something of the magnitude of power revocation BEFORE it is implemented in play...

If you are the DM and this is established as part of your world, ensure that players know this up front if they are considering playing a warlock (or any other class likely to have powers revoked for any reason).

If you are a player and you want this to either be highly probable, talk with your DM. It can create an intriguing story.

Already covered

RAW, there isn't any explicit text that covers a warlock's powers being stripped. Also, there is no class that has rules text covering a loss of powers, save the Paladin whose powers change form when he becomes an Oathbreaker. (DMG p. 97)

Lore from stories associated with various pact-style magic demonstrates and sets precedent that it could be a good story hook, allowing for a very interesting story line that leads to all the things that were mentioned in the original question.

Also Consider

The power belongs to the entity to dole out. If they granted it, it is likely true that they could take it away. This is more of a reference to old literature, to what makes sense, and to what would be fun with the game you and your DM seem to be trying to build.

The rules do not state the specific pact, this is the part that cannot be stressed enough. The power that they currently have should mostly be considered as payment for services rendered. If they are not completely paid for (ongoing payment, for example), then try to avoid stripping a lot of their power from them. Make it minimal, but noticeable. Lower spell slot levels by one levels as that part hasn't been paid in full, if that helps the story line, but do not completely cripple the character.

As for the specific scenario posted in the question:

The devil is highly unlikely to strip power from someone if it is part of a contract. To do so is highly unorthodox for a devil, and would be looked at even more poorly than an upstart servant that the devil couldn't control. The devils live by their contracts, and although adding loop-holes may be favored, rescinding an agreement is not. If a devil were to rescind the power of one of their warlocks, it is likely that another entity would try to mock them by taking the contract instead. This is even more true of a relatively powerful warlock. That said, a devil is also very likely to add a hidden clause that prevents the warlock from using their powers against the devil, with revocation of powers being either temporary or permanent, depending on the devil, the warlock, and the devil's disposition at the time.

They will follow the letter of the contract completely, but don't care about the spirit of the contract. If the devil is powerful enough to grant powers as a patron, they are likely intelligent enough to be more careful about the contract, though a particularly savvy and/or intelligent character could manipulate them in to a contract that is written to the benefit of the character more than the patron (protecting themselves from abandoning the patron, for example).

If you really want to do it

The best way to add the possibility of power revocation for story-line purposes is to ensure that it is an active part of the party's story (as opposed to a passive one). Allow the party to try to stop the powers from getting revoked, or have another patron (possibly a more sinister one) inform the warlock that they are going to lose their powers and offer to be a surrogate patron.

Do something that directly involves the warlock in whether they lose or retain their powers.

In short

Is it possible? Rules don't state that it is, but this is something a DM could easily say yes to with good justification to back it up based on game world.

Should the DM take this path? Probably not, or at least not seriously. If he does, then he should offer a work-around. Don't strip power from a character/player without offering a way of obtaining it again. Don't make the game less fun.

You actually have a built in answer in your question.

"...she wrote that she is seeking out her patron so that it can help her fly over some ancient city walls."

When you couple that with:

"I explained to the player that fly is already a warlock spell that she will have access to at higher levels..."

Now, you want to know how to do that in game? Take on the role of her patron so that her patron explains to her that she WILL be able to fly over the walls as she desires, it will just require some more power. This is an excellent RP scenario for you to engage in with your player. As for hunter's mark, when your player starts talking about ways to single out foes and weaken them, the Patron should be bringing up the Warlock version of Hunter's Mark, which is called Hex.

As for the other classes, it's really up to them. Here's my personal breakdown, logically, of how they know about what spells they have access to:

1. Wizards - Through meticulous study of books and practical exercise.
2. Arcane Tricksters - Same as wizards (PHB covers this under the class)
3. Eldritch Knights - Same as wizards (PHB covers this under the class)
4. Bards - Through the colleges they attend. Their knowledge of magic can be either refined, or broad, based on their college of study.
5. Sorcerers - Since their power originates within them, I personally feel that they can sense the magics available to be tapped in the weave because they have a primal connection to it.
6. Warlocks - Their knowledge comes from their other-worldy patron. The warlock class has some access to casting, but more access to Invocations which act more akin to spell like abilities. They learn about their power from their actual source and have struck some kind of bargain to tap into it.
7. Divine Casters - This is Paladins, Rangers, Druids and Clerics. They pray to their gods. As they increase in power and knowledge of the world (level up), their gods grant them further insight into the Divine domains.

The Way of the Four Elements Monks aren't on the list above because they aren't actually spell casters. They have Discipline of the Elements instead, which functions very differently from spell casting in that it uses Ki points rather than spell slots. In addition, you select from a list of disciplines, not from a spell list.

But remember, that's my personal take on the source of magical power and knowledge that's only kind of backed up by the books in the sense of the Weave and the Divine. What's really great about the D&D multiverse is that you don't need to subscribe to the concept of the Weave and the Divine at all. You can play a game in our world, where magic is granted by the Egyptian Pantheon. Or you can play in a Final Fantasy setting where magic comes from sources like materia. Or you can tap other materials as sources of magic, like dragon souls, energy fonts, sheer willpower, or radiation.

The possibilities are limitless. It's up to you, and your players, to describe how they know about certain things and whether or not that makes sense consistently within your game world.